FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: PZ4NP

Calculation Name: 3FMM-A-Xray12

Preferred Name: MAP kinase p38 alpha

Target Type: SINGLE PROTEIN

Ligand Name: 6-(2,4-difluorophenoxy)-n-[(1r)-1-methyl-2-(methylsulfonyl)ethyl]-1h-pyrazolo[3,4-d]pyrimidin-3-amine

ligand 3-letter code: XI2

PDB ID: 3FMM

Chain ID: A

ChEMBL ID: CHEMBL260

UniProt ID: Q16539

Base Structure: X-ray

Registration Date: 2017-08-22

Reference:

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement MOE:Homology modeling
Water No
Procedure Auto-FMO protocol ver. 1.20160629
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 347
LigandResidueName XI2
LigandFragmentNumber 347
LigandCharge
Software MIZUHO/ABINIT-MP 4.0(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -5755414.549057
FMO2-HF: Nuclear repulsion 5614788.490419
FMO2-HF: Total energy -140626.058638
FMO2-MP2: Total energy -141035.263176


3D Structure
Snapshot
 
Ligand structure

XI2

ligand structure
Ligand Interaction
ligand interaction
Ligand binding energy
"
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
-131.135-100.28185.595-39.196-77.2600.050


Interactive mode: IFIE and PIEDA for fragment #347(A:361:XI2)


Summations of interaction energy for fragment #347(A:361:XI2)
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
-131.135-100.28185.595-39.196-77.26-0.05
Interaction energy analysis for fragmet #347(A:361:XI2)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.049 / q_NPA : -0.028
Distance from base fragment(s) [Å]
Dist
Interaction energy by IFIE and PIEDA
[kcal/mol]
| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >
Fragment charge [e]
FCHARGE q_Mulliken
q_NPA q(I=>J)
Residue
Res #    RES   
Sort
Graph Options
X Axis Label
Y Axis Max Y Axis Min
Display   
frag_NumFragment number. ChainChain species. Res #Residue number. RES3-letter code of amino acid residue, ligand and solvent molecule. FCHARGEFormal charge [e]. q_MullikenFragment charge evaluated by Mulliken charge [e]. q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e]. DISTDistance from Ligand [Å]. TotalIFIE at MP2 level [kcal/mol]. ESElectro static interaction energy by PIEDA [kcal/mol]. EXExchange-repulsion energy by PIEDA [kcal/mol]. CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol]. DI(MP2)Dispersion energy by PIEDA [kcal/mol]. q(I=>J)Charge transfer value from I to J fragmens [e].
1A6PRO10.8490.90115.299-0.133-0.1330.0000.0000.0000.000
2A7THR00.0840.06118.3660.0240.0240.0000.0000.0000.000
3A8PHE00.0150.01313.078-0.034-0.0340.0000.0000.0000.000
4A9TYR0-0.035-0.02914.3190.0080.0080.0000.0000.0000.000
5A10ARG10.9440.97116.017-0.634-0.6340.0000.0000.0000.000
6A11GLN00.0530.02514.710-0.120-0.1200.0000.0000.0000.000
7A12GLU-1-0.982-0.97815.8161.3391.3390.0000.0000.0000.000
8A13LEU0-0.006-0.00811.0400.0150.0150.0000.0000.0000.000
9A14ASN00.0250.0169.479-0.238-0.2380.0000.0000.0000.000
10A15LYS10.9370.95513.379-1.634-1.6340.0000.0000.0000.000
11A16THR00.0020.02212.845-0.201-0.2010.0000.0000.0000.000
12A17ILE00.025-0.00515.3400.0570.0570.0000.0000.0000.000
13A18TRP0-0.046-0.0336.437-0.153-0.1530.0000.0000.0000.000
14A19GLU-1-0.909-0.96413.0950.5350.5350.0000.0000.0000.000
15A20VAL00.0100.0069.8140.0110.0110.0000.0000.0000.000
16A21PRO0-0.032-0.01111.140-0.060-0.0600.0000.0000.0000.000
17A22GLU-1-0.866-0.95313.6030.1750.1750.0000.0000.0000.000
18A23ARG10.7770.88512.0870.4020.4020.0000.0000.0000.000
19A24TYR0-0.051-0.0399.063-0.149-0.1490.0000.0000.0000.000
20A25GLN00.0220.01012.1890.1950.1950.0000.0000.0000.000
21A26ASN0-0.020-0.02212.1850.0190.0190.0000.0000.0000.000
22A27LEU00.0030.0119.7440.0110.0110.0000.0000.0000.000
23A28SER0-0.019-0.0107.6950.1340.1340.0000.0000.0000.000
24A29PRO00.0100.0036.8820.3610.3610.0000.0000.0000.000
25A30VAL00.0070.0082.634-3.101-1.0521.599-0.928-2.7200.010
26A31GLY00.0570.0053.479-0.0951.1570.150-0.392-1.0090.002
27A32SER0-0.064-0.0243.780-4.171-3.7940.037-0.130-0.2830.002
28A33GLY0-0.0020.0017.052-1.249-1.2490.0000.0000.0000.000
29A34ALA0-0.026-0.0096.098-0.400-0.4000.0000.0000.0000.000
30A35TYR00.008-0.0082.498-14.202-8.0848.890-3.578-11.430-0.014
31A36GLY0-0.0040.0144.7671.7691.908-0.001-0.015-0.1240.000
32A37SER0-0.060-0.0407.2110.3600.3600.0000.0000.0000.000
33A38VAL00.0290.0082.707-4.998-1.4670.901-1.410-3.0230.014
34A39CYS0-0.054-0.0055.029-0.518-0.326-0.001-0.011-0.1800.000
35A40ALA00.0340.0334.253-0.445-0.293-0.001-0.015-0.1370.000
36A41ALA00.009-0.0036.1910.2770.2770.0000.0000.0000.000
37A42PHE0-0.006-0.0029.363-0.491-0.4910.0000.0000.0000.000
38A43ASP-1-0.705-0.81010.210-0.380-0.3800.0000.0000.0000.000
39A44THR0-0.046-0.04312.165-0.091-0.0910.0000.0000.0000.000
40A45LYS10.8790.94014.5290.1840.1840.0000.0000.0000.000
41A46THR00.019-0.01312.204-0.047-0.0470.0000.0000.0000.000
42A47GLY0-0.0080.00914.500-0.053-0.0530.0000.0000.0000.000
43A48LEU00.0030.0138.976-0.144-0.1440.0000.0000.0000.000
44A49ARG10.9490.9747.7552.3722.3720.0000.0000.0000.000
45A50VAL00.010-0.0045.404-0.568-0.5680.0000.0000.0000.000
46A51ALA0-0.001-0.0052.771-2.0700.4822.192-1.348-3.3970.010
47A52VAL0-0.006-0.0072.701-6.216-3.6850.646-1.222-1.955-0.011
48A53LYS10.8660.9202.393-8.013-3.9663.729-2.397-5.3780.020
49A54LYS10.8930.9654.055-3.375-3.0250.008-0.075-0.2820.001
50A55LEU0-0.010-0.0087.2880.4960.4960.0000.0000.0000.000
51A56SER0-0.027-0.0199.619-0.323-0.3230.0000.0000.0000.000
52A57ARG10.9090.95112.613-1.295-1.2950.0000.0000.0000.000
53A58PRO00.0530.04012.433-0.044-0.0440.0000.0000.0000.000
54A59PHE00.0590.01514.056-0.097-0.0970.0000.0000.0000.000
55A60GLN00.0070.00817.271-0.126-0.1260.0000.0000.0000.000
56A61SER00.004-0.04019.695-0.066-0.0660.0000.0000.0000.000
57A62ILE00.0790.03219.8420.0270.0270.0000.0000.0000.000
58A63ILE00.0170.01417.957-0.011-0.0110.0000.0000.0000.000
59A64HIS0-0.0020.02515.564-0.047-0.0470.0000.0000.0000.000
60A65ALA00.0530.03714.9390.0460.0460.0000.0000.0000.000
61A66LYS10.8630.94215.395-0.172-0.1720.0000.0000.0000.000
62A67ARG10.9220.9659.475-1.573-1.5730.0000.0000.0000.000
63A68THR0-0.033-0.02910.8130.0540.0540.0000.0000.0000.000
64A69TYR00.0250.02210.430-0.075-0.0750.0000.0000.0000.000
65A70ARG10.8020.86211.231-0.247-0.2470.0000.0000.0000.000
66A71GLU-1-0.824-0.8975.0621.5371.659-0.001-0.004-0.1180.000
67A72LEU0-0.017-0.0016.766-0.348-0.3480.0000.0000.0000.000
68A73ARG10.8680.9268.2700.0200.0200.0000.0000.0000.000
69A74LEU0-0.032-0.0088.007-0.093-0.0930.0000.0000.0000.000
70A75LEU0-0.008-0.0172.389-2.065-0.9231.320-0.568-1.893-0.004
71A76LYS10.7850.8715.8730.1450.1450.0000.0000.0000.000
72A77HIS0-0.052-0.0178.956-0.060-0.0600.0000.0000.0000.000
73A78MET0-0.076-0.0197.5650.0020.0020.0000.0000.0000.000
74A79LYS10.9430.9708.9350.5810.5810.0000.0000.0000.000
75A80HIS00.0990.04710.818-0.041-0.0410.0000.0000.0000.000
76A81GLU-1-0.826-0.89711.041-1.839-1.8390.0000.0000.0000.000
77A82ASN0-0.019-0.01310.554-0.133-0.1330.0000.0000.0000.000
78A83VAL0-0.032-0.0147.860-0.114-0.1140.0000.0000.0000.000
79A84ILE0-0.044-0.0122.656-2.020-0.4211.005-0.497-2.1080.001
80A85GLY00.0900.0415.4280.1080.1080.0000.0000.0000.000
81A86LEU0-0.078-0.0332.769-1.194-0.1280.334-0.418-0.9830.003
82A87LEU0-0.0030.0015.024-0.263-0.142-0.001-0.003-0.1180.000
83A88ASP-1-0.842-0.9105.546-0.015-0.0150.0000.0000.0000.000
84A89VAL0-0.018-0.0015.1890.3280.386-0.001-0.003-0.0540.000
85A90PHE0-0.0120.0027.261-0.081-0.0810.0000.0000.0000.000
86A91THR00.018-0.01310.2170.1540.1540.0000.0000.0000.000
87A92PRO0-0.011-0.00313.053-0.079-0.0790.0000.0000.0000.000
88A93ALA0-0.0370.00315.912-0.042-0.0420.0000.0000.0000.000
89A94ARG10.9420.95818.032-0.308-0.3080.0000.0000.0000.000
90A95SER00.0140.00720.826-0.030-0.0300.0000.0000.0000.000
91A96LEU00.0770.03619.6870.0460.0460.0000.0000.0000.000
92A97GLU-1-0.938-0.99320.8710.2940.2940.0000.0000.0000.000
93A98GLU-1-0.921-0.94620.9610.3970.3970.0000.0000.0000.000
94A99PHE0-0.105-0.03413.0370.0730.0730.0000.0000.0000.000
95A100ASN0-0.019-0.03316.773-0.023-0.0230.0000.0000.0000.000
96A101ASP-1-0.923-0.94612.4731.2891.2890.0000.0000.0000.000
97A102VAL00.007-0.0127.670-0.151-0.1510.0000.0000.0000.000
98A103TYR00.0160.0106.7950.4750.4750.0000.0000.0000.000
99A104LEU00.0160.0042.404-2.313-0.6271.918-1.306-2.2980.012
100A105VAL00.0140.0152.406-6.403-4.0852.303-1.683-2.938-0.015
101A106THR00.0160.0072.305-3.7860.1805.594-2.305-7.2560.007
102A107HIS00.1010.0384.104-0.8020.0330.004-0.353-0.487-0.001
103A108LEU0-0.053-0.0151.758-18.610-20.80315.337-5.862-7.282-0.042
104A109MET0-0.003-0.0041.779-5.186-17.08425.124-7.048-6.1780.039
105A110GLY00.0490.0221.868-24.647-24.59210.162-4.524-5.692-0.067
106A111ALA0-0.023-0.0112.525-2.1370.7831.102-1.570-2.452-0.012
107A112ASP-1-0.812-0.8902.528-8.439-6.9540.699-0.320-1.864-0.011
108A113LEU00.0590.0183.9811.6311.7980.009-0.027-0.1490.000
109A114ASN0-0.006-0.0027.1350.7160.7160.0000.0000.0000.000
110A115ASN0-0.036-0.0184.7741.3281.401-0.001-0.001-0.0720.000
111A116ILE0-0.031-0.0087.3230.5580.5580.0000.0000.0000.000
112A117VAL00.0280.00910.0470.3950.3950.0000.0000.0000.000
113A118LYS10.8990.96511.5781.2391.2390.0000.0000.0000.000
114A119CYS0-0.066-0.03614.0550.1160.1160.0000.0000.0000.000
115A120GLN0-0.052-0.01816.361-0.024-0.0240.0000.0000.0000.000
116A121LYS10.9300.96917.8850.4150.4150.0000.0000.0000.000
117A122LEU00.0310.02614.075-0.016-0.0160.0000.0000.0000.000
118A123THR0-0.033-0.02318.7500.1000.1000.0000.0000.0000.000
119A124ASP-1-0.766-0.90220.054-0.803-0.8030.0000.0000.0000.000
120A125ASP-1-0.836-0.90821.049-1.059-1.0590.0000.0000.0000.000
121A126HIS00.0660.03515.9450.0180.0180.0000.0000.0000.000
122A127VAL0-0.044-0.02216.388-0.155-0.1550.0000.0000.0000.000
123A128GLN0-0.0070.01017.674-0.084-0.0840.0000.0000.0000.000
124A129PHE00.0680.04114.374-0.021-0.0210.0000.0000.0000.000
125A130LEU0-0.003-0.00710.896-0.124-0.1240.0000.0000.0000.000
126A131ILE0-0.021-0.02714.009-0.073-0.0730.0000.0000.0000.000
127A132TYR0-0.015-0.01116.336-0.016-0.0160.0000.0000.0000.000
128A133GLN00.0150.00712.655-0.127-0.1270.0000.0000.0000.000
129A134ILE0-0.031-0.00911.987-0.012-0.0120.0000.0000.0000.000
130A135LEU0-0.005-0.00814.2050.0970.0970.0000.0000.0000.000
131A136ARG10.8180.91716.0461.4461.4460.0000.0000.0000.000
132A137GLY00.0140.00313.8120.0530.0530.0000.0000.0000.000
133A138LEU0-0.042-0.03814.2010.0930.0930.0000.0000.0000.000
134A139LYS10.8680.93715.9030.8710.8710.0000.0000.0000.000
135A140TYR00.0370.03011.9760.0740.0740.0000.0000.0000.000
136A141ILE00.0250.01310.7670.0960.0960.0000.0000.0000.000
137A142HIS0-0.103-0.07814.3730.1150.1150.0000.0000.0000.000
138A143SER0-0.068-0.02717.5640.0870.0870.0000.0000.0000.000
139A144ALA00.0220.01615.2680.0510.0510.0000.0000.0000.000
140A145ASP-1-0.934-0.96917.320-0.355-0.3550.0000.0000.0000.000
141A146ILE0-0.052-0.01012.0740.0660.0660.0000.0000.0000.000
142A147ILE0-0.038-0.03015.443-0.035-0.0350.0000.0000.0000.000
143A148HIS0-0.030-0.0268.9160.2050.2050.0000.0000.0000.000
144A149ARG10.9070.93612.7690.3630.3630.0000.0000.0000.000
145A150ASP-1-0.858-0.94612.3340.0960.0960.0000.0000.0000.000
146A151LEU00.0490.05211.109-0.014-0.0140.0000.0000.0000.000
147A152LYS10.8970.9419.9810.2160.2160.0000.0000.0000.000
148A153PRO00.0660.0369.344-0.315-0.3150.0000.0000.0000.000
149A154SER00.004-0.0096.063-0.628-0.6280.0000.0000.0000.000
150A155ASN0-0.046-0.0224.924-0.941-0.871-0.001-0.006-0.0630.000
151A156LEU00.0240.0246.1790.1640.1640.0000.0000.0000.000
152A157ALA00.0100.0042.735-1.783-1.0410.404-0.224-0.9230.001
153A158VAL0-0.011-0.0123.8081.9262.1380.0030.017-0.2330.000
154A159ASN0-0.050-0.0255.425-2.162-2.1620.0000.0000.0000.000
155A160GLU-1-0.925-0.9827.781-3.817-3.8170.0000.0000.0000.000
156A161ASP-1-0.896-0.92810.601-1.790-1.7900.0000.0000.0000.000
157A162CYS0-0.096-0.06510.6620.3160.3160.0000.0000.0000.000
158A163GLU-1-0.861-0.90510.756-2.374-2.3740.0000.0000.0000.000
159A164LEU0-0.034-0.0248.099-0.814-0.8140.0000.0000.0000.000
160A165LYS10.8700.9255.4953.9133.9130.0000.0000.0000.000
161A166ILE0-0.019-0.0096.786-0.579-0.5790.0000.0000.0000.000
162A167LEU00.008-0.0022.323-3.748-0.8342.134-0.965-4.0830.005
163A168ASP-1-0.934-0.9674.3582.0282.132-0.001-0.005-0.0980.000
164A169PHE00.0000.0125.8920.3740.3740.0000.0000.0000.000
165A170GLY00.0330.0108.7820.0390.0390.0000.0000.0000.000
166A171LEU0-0.055-0.0387.6580.1890.1890.0000.0000.0000.000
167A172ALA0-0.045-0.00910.7800.1570.1570.0000.0000.0000.000
168A173ARG10.7590.86112.5310.1680.1680.0000.0000.0000.000
169A174HIS0-0.032-0.02311.9370.1550.1550.0000.0000.0000.000
170A175THR0-0.018-0.00315.718-0.139-0.1390.0000.0000.0000.000
171A176ASP-1-0.889-0.95319.3320.3160.3160.0000.0000.0000.000
172A177ASP-1-0.935-0.95421.9190.5840.5840.0000.0000.0000.000
173A178GLU-1-0.780-0.87816.3880.9960.9960.0000.0000.0000.000
174A179MET0-0.0710.00818.270-0.093-0.0930.0000.0000.0000.000
175A180THR0-0.030-0.01920.312-0.103-0.1030.0000.0000.0000.000
176A181GLY00.0230.01422.0010.0340.0340.0000.0000.0000.000
177A182TYR0-0.011-0.00220.970-0.054-0.0540.0000.0000.0000.000
178A183VAL00.0100.01717.3650.0340.0340.0000.0000.0000.000
179A184ALA00.0600.01313.641-0.054-0.0540.0000.0000.0000.000
180A185THR0-0.080-0.08413.649-0.157-0.1570.0000.0000.0000.000
181A186ARG10.8700.91315.351-0.122-0.1220.0000.0000.0000.000
182A187TRP0-0.0330.00716.557-0.063-0.0630.0000.0000.0000.000
183A188TYR0-0.046-0.05914.131-0.025-0.0250.0000.0000.0000.000
184A189ARG10.8670.95716.9540.0160.0160.0000.0000.0000.000
185A190ALA00.0600.03019.7140.0100.0100.0000.0000.0000.000
186A191PRO00.0120.00622.8820.0460.0460.0000.0000.0000.000
187A192GLU-1-0.757-0.87424.780-0.237-0.2370.0000.0000.0000.000
188A193ILE0-0.0070.00619.2980.0310.0310.0000.0000.0000.000
189A194MET0-0.074-0.01623.2610.0440.0440.0000.0000.0000.000
190A195LEU0-0.010-0.01624.3280.0430.0430.0000.0000.0000.000
191A196ASN0-0.043-0.01324.846-0.008-0.0080.0000.0000.0000.000
192A197TRP00.001-0.00227.164-0.002-0.0020.0000.0000.0000.000
193A198MET0-0.017-0.02827.7800.0000.0000.0000.0000.0000.000
194A199HIS00.0160.01923.8630.0180.0180.0000.0000.0000.000
195A200TYR00.0230.02319.259-0.023-0.0230.0000.0000.0000.000
196A201ASN00.0880.07522.703-0.028-0.0280.0000.0000.0000.000
197A202GLN00.0730.01119.573-0.003-0.0030.0000.0000.0000.000
198A203THR0-0.001-0.03820.014-0.047-0.0470.0000.0000.0000.000
199A204VAL0-0.044-0.01918.561-0.011-0.0110.0000.0000.0000.000
200A205ASP-1-0.699-0.83716.056-0.705-0.7050.0000.0000.0000.000
201A206ILE0-0.025-0.00618.298-0.089-0.0890.0000.0000.0000.000
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